Federal Environment Minister Tony Burke says negotiations with the states and territories on the management of the Murray-Darling system have reached a higher level of agreement than ever before.

Officials worked into the night to agree on a framework covering how the amount of water returned to the system could be adjusted, but there is still no agreement on the starting point - exactly how much water should be returned.

Monday was the deadline for the states to respond to the revised draft plan on the Murray-Darling Basin.

Mr Burke says they worked right up to that deadline.

"What happened yesterday was, and some would say fairly unexpectedly, as negotiations went on right through into the evening, we ended up in a situation where we had a document that all the jurisdictions could sign on to that effectively provides the design of how the reform would run," he said.

That document is the Ministerial Council's response to the revised plan issued by the Murray-Darling Basin Authority (MDBA) in May.

Mr Burke says it outlines, for the first time, a consensus on how environmental water that is returned to the system will be managed.

"While we're still a fair way short of where I need to get to later this year in terms of the exact final pathway for a Murray-Darling Basin plan, what we do have now is a higher level of agreement than we've ever had," he said.

"The basic structure is now agreed and able to be put in place as to what that reform would look like."

Victorian Water Minister Peter Walsh says it is all about working smarter.

That includes recognising that up to 650 gigalitres could be found through better and more efficient delivery of environmental water.

"And that is about having works and measures like South Australia is doing with Chowilla, and like is being done at Hattah Lakes at the moment, so those sorts of works can achieve good environmental outcomes with less water," he said.

"So you don't need major floods to achieve the flooding to get the outcome and there's opportunities in how we actually run the river system to be smarter and again create effectively better use of water."

Sticking point

But there is still the sticking point of how much water should be put back into the river.

The revised plan is modelled on a figure of 2,750 gigalitres.

Upstream states say that is too much, while downstream states, including South Australian Water Minister Paul Caica, say they want more.

"What happened over the last five weeks is that certain agreements were reached between the states and the Commonwealth with respect to, amongst other things, how the system will be managed," Mr Caica said.

"But critical to that is that we believe that the total quantity of water that is required has not been determined, and we do say that 2,750 gigalitres is not enough; we made that very clear.

"What happens (now) is those areas of agreement will be communicated to the authority by the Federal Government, appended to that will be the various state submissions that are essentially areas of disagreement.

"We would say that those areas of disagreement are greater in number than what is agreed."

Mr Burke concedes there are still a large number of issues to be agreed on.

"The truth is there have been a million sticking points that have prevented us from running the basin as a national system for a century now, and every one of these issues is a significant hurdle to get past," he said.

Once the MDBA has reviewed the responses it will reply to the minister.

He can then seek feedback from the states again before taking the final plan to Cabinet.